RNA-seq of Rice Yellow Stem BorerScirpophaga incertulasReveals Molecular Insights During Four Larval Developmental Stages

Abstract

The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.

Refining the phylogeny of Crambidae with complete sampling of subfamilies (Lepidoptera, Pyraloidea)

“…We provide the first phylogeny comprising all subfamilies of Crambidae and including pyraloid molecular data sets from major previous phylogenetic studies (Heikkilä et al., 2015; Kawahara & Breinholt, 2014; Léger et al., 2019; Mally et al., 2019; Mutanen et al., 2010; Regier et al., 2012), from published genomes or transcriptomes (Challis et al., 2016; Renuka et al, 2017) and our own sequences. Our data set provides placement for Cathariinae, Cybalomiinae and Linostinae, although without well‐supported sister relationships.…”

“…A representative subset of the taxa from phylogenetic studies of Léger et al (2019) and Mally et al (2019) were also included. Sequences of interest were retrieved from published transcriptomes of Cnaphalocrocis medinalis (Guenée, 1854), Myelobia smerintha (Hübner, 1821) (Kawahara & Breinholt, 2014) and Scirpophaga incertulas (Walker, 1863) (Renuka et al, 2017), and from the whole genomes of Amyelois transitella (Walker, 1863) and Chilo suppressalis (Walker, 1863) on the LepBase interface (Challis et al, 2016;ensembl.lepbase.org). Taxon sampling is summarized in Table S1.…”

Characterizing potential repelling volatiles for “push-pull” strategy against stem borer: a case study in Chilo auricilius

“…The identified CSPs were named after the CSPs from Bombyx mori [22]. To compare the CSPs expressed in C.auricilius with that in other closely related insect species, the phylogenetic analysis was performed by using previously reported CSPs in C. suppressalis [25], B.mori [22] , Scirpophaga incertulas [26] , Sesamia inferens [27] . Phylogenetic analysis showed that all the 92 CSPs from the five insect species revealed well-supported clades displaying clear orthologous relationships.…”

The Draft Genome of Yellow Stem Borer, an Agriculturally Important Pest, Provides Molecular Insights into Its Biology, Development and Specificity Towards Rice for Infestation

“…Adults of YSB were collected from one plot of ICAR-IIRR, Hyderabad farm, and females were selected based on the morphological features and were subjected to whole-genome sequencing [ 13 , 14 ]. The DNA was isolated from the female adult YSB using a standard CTAB method and checked for quality and quantity on 0.8% agarose gel and Nanodrop, respectively.…”